Since microbial gene sequencing was utilized for etiologic diagnosis of culture-negative endocarditis, cases of Bartonella endocarditis have been reported in various countries. Herein we report the first case of Bartonella quintana endocarditis, which was confirmed for the first time in Korea by 16S rRNA gene sequencing from the excised valve. A 75-yr-old woman was hospitalized due to dyspnea. Echocardiography demonstrated large oscillating vegetation at the aortic valve. Blood culture was negative. She underwent valve replacement and sequencing of the 16S rRNA gene from excised valve identified Bartonella quintana. She was successfully treated with combined use of ceftriaxone and gentamicin.